Yellow Sigatoka disease caused by Cercospora musae, is an economically important disease of banana (Musa spp.). It is a serious constraint predominantly for the popular Cavendish cultivars and management is highly dependent on the use of fungicides. There are certain cultivars of banana which are resistant to Yellow Sigatoka. However, molecular studies in interactions between the resistant cultivars with the pathogen are limited. Exploring an incompatible interaction would not only provide information on adequate defense mechanisms but also assist in the development of new control approaches. For the present study, the resistant cultivar Musa paradisiaca cv. Kachkal was selected, which has been reported to have resistance to Sigatoka in Assam (India). Identification of defense related genes deferentially expressed during the incompatible Cercospora musae- Kachkal interaction will contribute towards development of cultivars resistant to the disease.